MArrayLM-class {limma} | R Documentation |
A list-based class for storing the results of fitting gene-wise linear models to a batch of microarrays.
Objects are normally created by lmFit
.
MArrayLM
objects do not contain any slots (apart from .Data
) but they should contain the following list components:
coefficients
:matrix
containing fitted coefficients or contrasts
stdev.unscaled
:matrix
containing unscaled standard deviations of the coefficients or contrasts
sigma
:numeric
vector containing residual standard deviations for each gene
df.residual
:numeric
vector containing residual degrees of freedom for each gene
Objects may also contain the following optional components:
Amean
:numeric
vector containing the average log-intensity for each probe over all the arrays in the original linear model fit.
Note this vector does not change when a contrast is applied to the fit using contrasts.fit
.
genes
:data.frame
containing gene names and annotation
design
:design matrix
of full column rank
contrasts
:matrix
defining contrasts of coefficients for which results are desired
F
:numeric
vector giving moderated F-statistics for testing all contrasts equal to zero
F.p.value
:numeric
vector giving p-value corresponding to F.stat
s2.prior
:numeric
value giving empirical Bayes estimated prior value for residual variances
df.prior
:numeric
vector giving empirical Bayes estimated degrees of freedom associated with s2.prior
for each gene
s2.post
:numeric
vector giving posterior residual variances
t
:matrix
containing empirical Bayes t-statistics
var.prior
:numeric
vector giving empirical Bayes estimated prior variance for each true coefficient
cov.coefficients
:numeric matrix
giving the unscaled covariance matrix of the estimable coefficients
pivot
:integer
vector giving the order of coefficients in cov.coefficients
. Is computed by the QR-decomposition of the design matrix.
If there are no weights and no missing values, then the MArrayLM
objects returned by lmFit
will also contain the QR-decomposition of the design matrix, and any other components returned by lm.fit
.
RGList
objects will return dimensions and hence functions such as dim
, nrow
and ncol
are defined.
MArrayLM
objects inherit a show
method from the virtual class LargeDataObject
.
The functions ebayes
and classifyTestsF
accept MArrayLM
objects as arguments.
Gordon Smyth
02.Classes gives an overview of all the classes defined by this package.